{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3292ERTL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3292ERTL",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinA_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3292ERTL](/measurement-sets/IGVFDS3292ERTL/) has in progress subobject auxiliary set [IGVFDS3747JQWV](/auxiliary-sets/IGVFDS3747JQWV/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3292ERTL/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8589BNCG](/in-vitro-systems/IGVFSM8589BNCG/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8589BNCG/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3292ERTL](/measurement-sets/IGVFDS3292ERTL/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS3292ERTL/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3747JQWV](/auxiliary-sets/IGVFDS3747JQWV/) has sequence file(s) [IGVFFI0820VFVE](/sequence-files/IGVFFI0820VFVE/), [IGVFFI3161QBSF](/sequence-files/IGVFFI3161QBSF/), [IGVFFI2443GAAZ](/sequence-files/IGVFFI2443GAAZ/), [IGVFFI0040XZWD](/sequence-files/IGVFFI0040XZWD/), [IGVFFI5702JKVQ](/sequence-files/IGVFFI5702JKVQ/), [IGVFFI9951WYGN](/sequence-files/IGVFFI9951WYGN/), [IGVFFI9664CLJX](/sequence-files/IGVFFI9664CLJX/), [IGVFFI1985BIQF](/sequence-files/IGVFFI1985BIQF/), [IGVFFI5853ZPCX](/sequence-files/IGVFFI5853ZPCX/), [IGVFFI9615CRFI](/sequence-files/IGVFFI9615CRFI/), [IGVFFI9055UTKW](/sequence-files/IGVFFI9055UTKW/), [IGVFFI2825GUDQ](/sequence-files/IGVFFI2825GUDQ/), [IGVFFI1945XLZA](/sequence-files/IGVFFI1945XLZA/), [IGVFFI3462JRZD](/sequence-files/IGVFFI3462JRZD/), [IGVFFI2197VNQV](/sequence-files/IGVFFI2197VNQV/), [IGVFFI4485SIXV](/sequence-files/IGVFFI4485SIXV/), [IGVFFI6867ZRQN](/sequence-files/IGVFFI6867ZRQN/), [IGVFFI5515QYPK](/sequence-files/IGVFFI5515QYPK/), [IGVFFI8953CKTP](/sequence-files/IGVFFI8953CKTP/), [IGVFFI5939OELQ](/sequence-files/IGVFFI5939OELQ/), [IGVFFI2514RVVW](/sequence-files/IGVFFI2514RVVW/), [IGVFFI2444PMIR](/sequence-files/IGVFFI2444PMIR/), [IGVFFI2754VLKH](/sequence-files/IGVFFI2754VLKH/), [IGVFFI3799HSPW](/sequence-files/IGVFFI3799HSPW/), [IGVFFI6071RMWJ](/sequence-files/IGVFFI6071RMWJ/), [IGVFFI9017OKIR](/sequence-files/IGVFFI9017OKIR/), [IGVFFI0024MOIX](/sequence-files/IGVFFI0024MOIX/), [IGVFFI3222ZSUX](/sequence-files/IGVFFI3222ZSUX/), [IGVFFI8813YRLM](/sequence-files/IGVFFI8813YRLM/), [IGVFFI0063TLFK](/sequence-files/IGVFFI0063TLFK/), [IGVFFI3509IPHZ](/sequence-files/IGVFFI3509IPHZ/), [IGVFFI3478AVNO](/sequence-files/IGVFFI3478AVNO/), [IGVFFI1835LTWU](/sequence-files/IGVFFI1835LTWU/), [IGVFFI7446TNTI](/sequence-files/IGVFFI7446TNTI/), [IGVFFI7269QVUI](/sequence-files/IGVFFI7269QVUI/), [IGVFFI9547ACQB](/sequence-files/IGVFFI9547ACQB/), [IGVFFI9708XWAB](/sequence-files/IGVFFI9708XWAB/), [IGVFFI0342DKCL](/sequence-files/IGVFFI0342DKCL/), [IGVFFI1033CNHF](/sequence-files/IGVFFI1033CNHF/), [IGVFFI2262YHUW](/sequence-files/IGVFFI2262YHUW/), [IGVFFI7618LDEQ](/sequence-files/IGVFFI7618LDEQ/), [IGVFFI1760WOHV](/sequence-files/IGVFFI1760WOHV/), [IGVFFI7793ZCKR](/sequence-files/IGVFFI7793ZCKR/), [IGVFFI3056QAUB](/sequence-files/IGVFFI3056QAUB/), [IGVFFI0014MJFW](/sequence-files/IGVFFI0014MJFW/), [IGVFFI5026EJMX](/sequence-files/IGVFFI5026EJMX/), [IGVFFI8037YHXS](/sequence-files/IGVFFI8037YHXS/), [IGVFFI5950NUTA](/sequence-files/IGVFFI5950NUTA/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3747JQWV/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3747JQWV](/auxiliary-sets/IGVFDS3747JQWV/) has sequence file(s): [IGVFFI0820VFVE](/sequence-files/IGVFFI0820VFVE/), [IGVFFI3161QBSF](/sequence-files/IGVFFI3161QBSF/), [IGVFFI2443GAAZ](/sequence-files/IGVFFI2443GAAZ/), [IGVFFI0040XZWD](/sequence-files/IGVFFI0040XZWD/), [IGVFFI5702JKVQ](/sequence-files/IGVFFI5702JKVQ/), [IGVFFI9951WYGN](/sequence-files/IGVFFI9951WYGN/), [IGVFFI9664CLJX](/sequence-files/IGVFFI9664CLJX/), [IGVFFI1985BIQF](/sequence-files/IGVFFI1985BIQF/), [IGVFFI5853ZPCX](/sequence-files/IGVFFI5853ZPCX/), [IGVFFI9615CRFI](/sequence-files/IGVFFI9615CRFI/), [IGVFFI9055UTKW](/sequence-files/IGVFFI9055UTKW/), [IGVFFI2825GUDQ](/sequence-files/IGVFFI2825GUDQ/), [IGVFFI1945XLZA](/sequence-files/IGVFFI1945XLZA/), [IGVFFI3462JRZD](/sequence-files/IGVFFI3462JRZD/), [IGVFFI2197VNQV](/sequence-files/IGVFFI2197VNQV/), [IGVFFI4485SIXV](/sequence-files/IGVFFI4485SIXV/), [IGVFFI6867ZRQN](/sequence-files/IGVFFI6867ZRQN/), [IGVFFI5515QYPK](/sequence-files/IGVFFI5515QYPK/), [IGVFFI8953CKTP](/sequence-files/IGVFFI8953CKTP/), [IGVFFI5939OELQ](/sequence-files/IGVFFI5939OELQ/), [IGVFFI2514RVVW](/sequence-files/IGVFFI2514RVVW/), [IGVFFI2444PMIR](/sequence-files/IGVFFI2444PMIR/), [IGVFFI2754VLKH](/sequence-files/IGVFFI2754VLKH/), [IGVFFI3799HSPW](/sequence-files/IGVFFI3799HSPW/), [IGVFFI6071RMWJ](/sequence-files/IGVFFI6071RMWJ/), [IGVFFI9017OKIR](/sequence-files/IGVFFI9017OKIR/), [IGVFFI0024MOIX](/sequence-files/IGVFFI0024MOIX/), [IGVFFI3222ZSUX](/sequence-files/IGVFFI3222ZSUX/), [IGVFFI8813YRLM](/sequence-files/IGVFFI8813YRLM/), [IGVFFI0063TLFK](/sequence-files/IGVFFI0063TLFK/), [IGVFFI3509IPHZ](/sequence-files/IGVFFI3509IPHZ/), [IGVFFI3478AVNO](/sequence-files/IGVFFI3478AVNO/), [IGVFFI1835LTWU](/sequence-files/IGVFFI1835LTWU/), [IGVFFI7446TNTI](/sequence-files/IGVFFI7446TNTI/), [IGVFFI7269QVUI](/sequence-files/IGVFFI7269QVUI/), [IGVFFI9547ACQB](/sequence-files/IGVFFI9547ACQB/), [IGVFFI9708XWAB](/sequence-files/IGVFFI9708XWAB/), [IGVFFI0342DKCL](/sequence-files/IGVFFI0342DKCL/), [IGVFFI1033CNHF](/sequence-files/IGVFFI1033CNHF/), [IGVFFI2262YHUW](/sequence-files/IGVFFI2262YHUW/), [IGVFFI7618LDEQ](/sequence-files/IGVFFI7618LDEQ/), [IGVFFI1760WOHV](/sequence-files/IGVFFI1760WOHV/), [IGVFFI7793ZCKR](/sequence-files/IGVFFI7793ZCKR/), [IGVFFI3056QAUB](/sequence-files/IGVFFI3056QAUB/), [IGVFFI0014MJFW](/sequence-files/IGVFFI0014MJFW/), [IGVFFI5026EJMX](/sequence-files/IGVFFI5026EJMX/), [IGVFFI8037YHXS](/sequence-files/IGVFFI8037YHXS/), [IGVFFI5950NUTA](/sequence-files/IGVFFI5950NUTA/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS3747JQWV/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3747JQWV](/auxiliary-sets/IGVFDS3747JQWV/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS3747JQWV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3747JQWV/",
"accession": "IGVFDS3747JQWV",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinA_AmpliconSequencing_AuxiliarySet"
],
"file_set_type": "variant sequencing"
}
],
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:39.932017+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS4359OODY/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:07:41.212296+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8589BNCG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8589BNCG",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinA"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 0-25% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "22",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T08:33:33.837858+00:00",
"summary": "prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "f637cecf-f002-49cd-bdac-8a03a123ffac"
}